The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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Variant: NM_000174.5(GP9):c.212T>G (p.Phe71Cys)

CA2602666

1491487 (ClinVar)

Gene: GP9 (HGNC:2815)
Condition: Bernard-Soulier syndrome (MONDO:0009276)
Inheritance Mode: Autosomal recessive inheritance
UUID: 0ff7deb4-f87f-4d5e-95c1-a7ad1a5bfa8d
Approved on: 2026-01-20
Published on: 2026-01-23

HGVS expressions

NM_000174.5:c.212T>G
NM_000174.5(GP9):c.212T>G (p.Phe71Cys)
NC_000003.12:g.129061951T>G
CM000665.2:g.129061951T>G
NC_000003.11:g.128780794T>G
CM000665.1:g.128780794T>G
NC_000003.10:g.130263484T>G
NG_008715.1:g.6150T>G
ENST00000307395.5:c.212T>G
ENST00000307395.4:c.212T>G
NM_000174.4:c.212T>G
More

Likely Pathogenic

Met criteria codes 3
PP4 PM2_Supporting PM3_Strong
Not Met criteria codes 3
PP3 PM5 BP4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Platelet Disorders Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for GP9 Version 1.1.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Platelet Disorders VCEP
The c.212T>G variant in GP9 is a missense variant predicted to cause substitution of Phenylalanine by Cysteine at amino acid 71 (p.Phe71Cys). At least one patient (Patient BS-23 in PMID:21699652) with this variant had aggregation absent for ristocetin and present for all other agonists, as well as less than 10% expression of GPIba measured by flow cytometry, which is highly specific for Bernard-Soulier syndrome. Additionally, the patient had excessive mucocutaneous bleeding which is consistent with Bernard-Soulier syndrome (PP4). This variant has been detected in at least three unrelated probands with Bernard-Soulier syndrome. Two of these individuals were homozygous for the variant (PMID:21699652, 1 PM3 point). One individual was compound heterozygous for this variant and the NM_000174.5(GP9):c.182A>G (p.Asn61Ser) which has been classified as Pathogenic by the PD VCEP. (1 PM3 point). These variants were confirmed in trans by family testing (2 PM3 points, PM3_Strong). The Grpmax filtering allele frequency in gnomaDv4.1 is 0 (based on 1/1179890 alleles) in the European (non-Finnish) population, which is below the <0.0000329 threshold for PM2_supporting. In summary, this variant meets the criteria to be classified as Likely Pathogenic for autosomal recessive Bernard-Soulier syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen PD VCEP: PP4, PM3, PM2_Supporting, PM3_Strong (VCEP specifications version 1).
Met criteria codes
PP4
At least one patient (Patient BS-23 in PMID:21699652) with this variant had aggregation absent for ristocetin and present for all other agonists, as well as less than 10% expression of GPIba measured by flow cytometry, which is highly specific for Bernard-Soulier syndrome. Additionally, the patient had excessive mucocutaneous bleeding which is consistent with Bernard-Soulier syndrome (PP4).
PM2_Supporting
The Grpmax filtering allele frequency in gnomaDv4.1 is 0 (based on 1/1179890 alleles) in the European (non-Finnish) population, which is below the <0.0000329 threshold for PM2_supporting.
PM3_Strong
This variant has been detected in at least three unrelated probands with Bernard-Soulier syndrome. Two of these individuals were homozygous for the variant (PMID:21699652, 1 PM3 point). One individual was compound heterozygous for this variant and the NM_000174.5(GP9):c.182A>G (p.Asn61Ser) which has been classified as Pathogenic by the PD VCEP. (1 PM3 point). These variants were confirmed in trans by family testing (2 PM3 points, PM3_Strong).
Not Met criteria codes
PP3
The computational predictor REVEL gives a score of 0.623, which is below the ClinGen PD VCEP PP3 threshold of >0.644 and does not predict a damaging effect on GP9 function. And the computational splicing predictor SpliceAI indicated that the variant has no predicted impact on splicing.
PM5
Another missense variant in the same codon has been reported in a patient with Bernard-Soulier syndrome c.212T>C (p.Phe71Ser) classified as likely pathogenic by the ClinGen PD VCEP, not considered here to avoid circularity.
BP4
The computational predictor REVEL gives a score of 0.623, which is above the ClinGen PD VCEP PP3 threshold of <0.290.
Curation History
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